[gmx-users] Regarding msd

pratibha kapoor kapoorpratibha7 at gmail.com
Wed Oct 8 08:08:39 CEST 2014

Please reply. Its really urgent. I have got comments from reviewer and
would have to resubmit the paper.

On Tue, Oct 7, 2014 at 10:03 PM, pratibha kapoor <kapoorpratibha7 at gmail.com>

> Hi all
> I have created my own code for msd calculation and would like to verify it
> from g_msd. I have created pdb files using trjconv -center -pbc whole
> option. Can I use the coordinates in pdb as such (with no
> wrapping/unwrapping/shifting) for running my code? or does the inbuild
> g_msd program modifies them (shift)?
> My msd values are not matching with the g_msd values. I suspect that
> discrepency in the pdb file creation since the values obtained from my
> program agrees with manual calculation (of some dummy values).
> Any suggestions are highly welcomed.

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